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Epigenetics

By Andrew Howley
Ever since the 1940s, the “modern synthesis” has presented evolution as the result of random mutations to DNA creating altered versions of living creatures that live and reproduce or die childless based on how well they happen to fit into their environment. This idea has served well in many ways for the generations since then, but now there’s a new kid in town.

Meet the “New” Kid

“Epigenetics” addresses the increasing evidence that things other than DNA can control the appearance and function of living things, can be passed on to future generations, and most importantly, can arise in direct response to external environmental conditions. It’s been covered in Science and TIME, on NOVA, Science Daily, and in an exposé-like series of articles from Scoop.co.nz.

This means that scientists should make room in the pantheon next to Darwin for the often ridiculed “stretch-your-neck-to-become-a-giraffe” Lamarck, who proposed that organisms change throughout their lives and pass on acquired traits to their offspring.

A closer look at history shows we also need to make a little more room next to Darwin for… Darwin himself.

The modern synthesis included certain of Darwin’s theories, but discarded others, including that of “pangenesis,” his idea that each body part somehow contributes “gemmules” of information to the sex cells to pass on traits acquired through use or disuse in the parent’s life (read Darwin’s “Provisional Hypothesis of Pangenesis”).

Tiny Prions, Major Changes

Recent work is showing that Darwin was more correct than he’s been given credit for. In “Epigenetics in the Extreme” from the October 29 Science magazine special issue on epigenetics, Randal Halfmann and Susan Lindquist discuss protein molecules called prions, which turn out to be remarkably similar to his hypothetical gemmules.

The magic happens when prions interact with the rest of the cell.

Prions are found inside cells and can take on different shapes, based on environmental conditions such as temperature or the presence of certain chemicals. Once altered, these proteins can bump into other prions and cause them to take on the new shape as well. When the cell divides, both daughter cells will contain prions of both states, and the chain reaction can keep occurring in that new generation.

The magic happens when prions interact with the rest of the cell, and even with DNA itself. The different shapes can cause different proteins to be made, or different parts of the DNA to be read or ignored, which can then trigger different actions or developments in the cell or the whole organism. If the external conditions change though, the other form of the prion will take precedence, and once again perform the original function.

Some may actually become incorporated into the DNA.

Halfmann and Lindquist even state that “these traits can ultimately become hardwired by subsequent genetic changes,” meaning some prion alterations may actually become incorporated into the DNA, thus blurring the line between genetics and epigenetics and raising intriguing chicken-and-egg type questions.

Whale-Size Implications

The broader implication of prions on epigenetic inheritance and evolution in general is that the ability to form different structures or perform different functions can be selected for at one time, and then kept around though unexpressed for generations, just waiting for the appropriate environmental trigger to reappear. When it is next expressed, other changes to the species may cause the original effect to take on slightly new forms, thus the organism responds to the environment with an existing toolkit, but continues to take on new appearances.

As a purely hypothetical example, the appearance of webbed fin-like appendages in birds or mammals in aquatic environments could thus be a result of the ancient fish-fin programming being kicked into a new usage as a result of a return to an ancestral environment.
Time for a More Modern Synthesis?

The overriding significance of these discoveries is that we now see concrete illustrations of how living things actively adapt to their environment even at a cellular level and can in at least some cases pass on those adaptations to their offspring. While theorized by many in the past, this is fairly new ground for modern discussions of evolution.

Prevailing view now clearly too narrow

The prevailing view that variation in a species is simply the result of a DNA program locked off from the world and altered only through random errors in transcription is now clearly too narrow. The study of epigenetics shows us that life and evolution are dynamic processes, based on the complex back-and-forth relationships between organisms and their entire environment.

And a Hint of Mind-Blowing Context

Finally, while these experiments and observations have been made mostly with single-celled organisms like yeast, or simpler animals like fruit flies, it’s important to remember that even the most advanced organisms are still made up of individual cells. Most remarkably, you yourself started out life as a single-celled organism, developing in an environment rich in chemical inputs and signals being produced by your mother in ever-changing response to her environment.

Epigenetics =
a) the study of heritable changes in gene function that do not involve changes in DNA sequence
b) the science of enduring changes in the pattern of gene activity, during embryo development and beyond, that do not involve alteration of the DNA sequence.

The “heritable or enduring changes” are epiDNAtics, not epigenetics. Alternative splicing is not epigenetics, even if/when not involving alteration of the DNA sequence. Earth life is an RNA world.

It’s the RNAs that evolve proteins. AND IT’S THE RNAs THAT HAVE EVOLVED AND PRODUCE AND EMPLOY THE DNA ( and RNA ) templates to carry out life processes, for enhancing Earth’s biosphere, for augmenting and constraining as long as possible some energy by augmenting its self-propagation, constraining some of the total energy of the universe, all of which is destined to fuel the ongoing cosmic expansion.